Humble Bundle - https://www.humblebundle.com/Kicking it off with probably the most popular bundle site, humble bundle works with charity and the developers. Pay what you want to get the games, pay more than the average to get the extra things!

Indie Royale - http://www.indieroyale.com/Another indie bundle site! Easy to use. Pay a minimum or pay more for bonus stuffs and knocking the price down for others!

Groupees - http://groupees.com/Groupees, now from time to time they run interesting bundles, including doujins! Now here's the interesting part, they list a bunch of games. You pick which ones you want! The more you add, the more the minimum price is!